[gmx-users] simulations of ice beginning to spin

Eric Smoll ericsmoll at gmail.com
Thu Aug 20 23:53:21 CEST 2015

Hello Nathan,

Did you set comm-mode and nstcomm
<http://manual.gromacs.org/online/mdp_opt.html#run> in your mdp file?


On Thu, Aug 20, 2015 at 3:37 PM, Nathan K Houtz <nhoutz at purdue.edu> wrote:

> Hello,
> I'm sorry to submit a query twice, but I have not received a reply since
> last week. The original message is below. As the subject line states, my
> simulations are developing a rotation that I cannot explain. I was
> wondering if the box size could be an issue, so I redid both simulations in
> NPT with the Parrinello-Rahman Barostat. It did not solve the rotation
> problem. Both outputs looked very similar to the results from NVT. In
> addition, the corners of the cubic simulation still became disordered.
> That's the only update I have. Please see below for further details. Thanks!
> Regards,
> Nathan
> ----- Original Message -----
> From: "Nathan K Houtz" <nhoutz at purdue.edu>
> To: "gromacs org gmx-users" <gromacs.org_gmx-users at maillist.sys.kth.se>
> Sent: Thursday, August 13, 2015 10:57:43 PM
> Subject: simulations of ice beginning to spin
> Hello,
> I am simulating two kinds of ice: ice Ih and ice Ic (cubic ice). Both
> simulations seem to have developed some rotation spontaneously and I'd like
> to know if I can control that somehow. I'm also simulating one in a
> triclinic box but the output gro file appears cubic. I'm not sure if I
> should be concerned about that or not. Lastly, the Ice Ic structure begins
> to fall apart during my simulation and I don't think it should. I'd
> appreciate help on any of these matters. Here are some more details:
> Ice Ih is done in a triclinic box, and originally looks like this:
> http://imgur.com/VQg9xQz. I use a rigid TIP4P/Ice water model,
> constrained by shake, and simulate it in NVT for 1,000,000 time steps (2
> ns) at a temperature of 217K and a density of 0.920 g/cm3. At the end, it
> looks like this: http://imgur.com/8uzddRH. First of all, I'm wondering if
> gromacs has correctly applied the triclinic box, as it appears that
> periodic boundary conditions have turned it into a cube. VMD is showing the
> box described by the .gro file. Secondly, it has been rotated, at least a
> few degrees, about the z axis. It did not noticeably rotate about the x or
> y axes. I'm not sure how to explain how the simulation would develop any
> angular momentum. In my .mdp file, I have gromacs get rid of angular
> momentum every 100 steps, but I don't think it should develop any in the
> first place. Any advice?
> The other simulation, ice ic, didn't go quite as well. Here is the
> original orientation, viewed from one of the corners:
> http://imgur.com/i0ncpju (I realize the orthographic projections make it
> harder to see the actual structure, but they make it easier to see unique
> patterns from various angles, which I'm trying to use to determine how it
> has rotated). This one was also simulated for 1,000,000 timesteps (2 ns) at
> 217K with TIP4P/Ice constrained by shake, but at a density of 0.931 g/cm3.
> The resulting structure is this: http://imgur.com/Lwl8UUw. I'm not sure
> I've got the exact corresponding orientation in this view here, but I
> believe it is. It's looking down the x-axis this time. This simulation got
> rotated much worse. Here are the before and after views looking down the
> z-axis, just like I showed for the ice Ih above: http://imgur.com/a/LRQR3.
> With such a large number of timesteps, I cannot output enough frames in the
> trajectory file to view this as a "smooth" movie and ide
>  ntify exactly when and why these rotations happen. It's more like a very
> long and rapid slide show. For the ice Ic, at least, it is possible that
> the whole box did not rotate, but all of the molecules simply reoriented
> themselves. But since at least part of the box appears to still be in the
> ice Ic structure, I'm not sure why they would do that. Ice Ic is only
> metastable at any temperature, so I would assume that if it falls apart,
> the structure would not come back. This is another issue. I would like to
> still have cubic ice structure at the end of this simulation, but clearly
> two of the corners have disastrously broken up. However, what looks like
> most of the molecules appear to still retain the structure. Do you think
> that it could be a problem with my box size, or the orientation? I'd like
> to know what things I might try to prevent the disintegration of the cubic
> structure.
> Thanks for any help. Regards,
> Nathan
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